Contacts of the strand formed by residues 115 - 122 (chain N) in PDB entry 6DZT


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with VAL 115 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59N  VAL      3.8     1.0    -      -       -      +
     60N  LYS*     3.6     1.6    -      -       -      -
     61N  GLN*     2.8    48.8    +      -       +      +
     63N  PRO*     6.2     2.0    -      -       +      -
    114N  ALA*     1.3    73.7    -      -       -      +
    116N  TYR*     1.3    62.8    +      -       -      +
    117N  TYR*     3.8    31.6    +      -       +      +
    134N  GLN      5.0     0.9    -      -       -      +
    135N  GLY*     4.0     7.0    -      -       -      -
    136N  THR      3.5    25.1    -      -       -      +
    137N  SER*     4.8    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 116 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28N  GLN*     2.8    21.9    +      -       -      -
     42N  MET*     3.8    22.7    -      -       +      -
     58N  TRP*     4.4     5.6    -      -       +      -
     59N  VAL      3.4     2.5    -      -       -      +
     60N  LYS*     3.9    30.6    +      -       +      -
     70N  ILE*     3.6    31.0    -      -       +      -
     86N  PHE*     5.5     1.3    -      +       -      -
    103N  MET*     4.2     8.1    -      -       +      -
    105N  LEU*     3.3    34.2    -      -       +      +
    112N  ASP*     3.5    31.5    +      -       -      -
    114N  ALA*     3.7    21.5    -      -       +      -
    115N  VAL*     1.3    71.8    -      -       -      +
    117N  TYR*     1.3    60.4    +      -       -      +
    135N  GLY*     4.3     0.2    -      -       -      -
    136N  THR*     3.3    18.2    +      -       -      +
    138N  VAL*     4.1    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 117 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28N  GLN*     4.0     3.8    -      -       -      +
     58N  TRP*     3.3    10.2    -      -       -      -
     59N  VAL*     2.9    38.2    +      -       +      +
     61N  GLN*     2.3    49.3    +      -       +      -
     67N  LEU*     4.3     8.1    -      -       +      -
    115N  VAL*     3.8    21.6    -      -       +      +
    116N  TYR*     1.3    73.5    -      -       -      +
    118N  CYS*     1.3    60.9    +      -       -      +
    132N  TRP*     3.6    30.5    -      +       +      -
    133N  GLY      3.3    22.0    -      -       -      +
    134N  GLN      3.9    11.7    -      -       -      -
    135N  GLY*     3.8     7.2    -      -       -      -
    196N  GLN*     2.9    14.7    +      -       -      -
    199N  TRP      6.0     0.2    -      -       -      -
    200N  LYS      3.9     3.3    +      -       -      -
    201N  SER*     3.8    22.0    -      -       -      -
    202N  PRO*     4.0     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 118 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26N  LEU*     3.5    10.9    -      -       -      +
     28N  GLN*     3.8    23.8    +      -       -      +
     44N  CYS*     2.0    48.2    -      -       -      -
     56N  ILE*     4.1     2.9    -      -       +      -
     57N  GLN      3.2     6.5    -      -       -      +
     58N  TRP*     3.7    23.3    -      -       +      -
    117N  TYR*     1.3    73.1    -      -       -      +
    119N  ALA*     1.3    60.5    +      -       -      +
    132N  TRP*     3.7     0.2    -      -       -      -
    133N  GLY*     2.8    27.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 119 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26N  LEU*     3.9     2.7    -      -       -      -
     56N  ILE*     3.4     2.3    -      -       -      -
     57N  GLN*     2.5    45.1    +      -       +      +
     59N  VAL*     4.7     1.1    -      -       +      -
    117N  TYR      4.2     0.4    +      -       -      -
    118N  CYS*     1.3    75.6    -      -       -      +
    120N  ARG*     1.3    61.9    +      -       -      +
    129N  LEU*     3.7    36.8    -      -       +      -
    131N  TYR      3.3     9.4    -      -       -      +
    132N  TRP*     3.9    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 120 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102D  GLU*     4.2     4.4    +      -       -      -
     24N  VAL*     3.6    15.2    -      -       -      +
     26N  LEU*     3.5    16.3    -      -       +      +
     49N  TYR*     3.4    60.5    -      -       -      +
     54N  TYR*     3.6    44.5    +      -       +      -
     55N  THR      3.7     4.7    -      -       -      +
     56N  ILE*     4.6     2.9    -      -       +      +
    119N  ALA*     1.3    72.1    -      -       -      +
    121N  LYS*     1.3    62.1    +      -       -      +
    129N  LEU*     3.3     4.2    -      -       -      -
    130N  ASP*     2.8    59.4    +      -       -      +
    131N  TYR*     2.8    34.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 121 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54N  TYR*     3.5     4.6    -      -       -      -
     55N  THR*     2.7    41.3    +      -       -      +
     57N  GLN*     3.5    35.4    -      -       +      +
    119N  ALA      3.8     0.2    +      -       -      -
    120N  ARG*     1.3    77.3    -      -       -      +
    122N  SER*     1.3    75.9    +      -       -      +
    123N  SER      4.9     0.8    -      -       -      -
    124N  ARG      3.1    19.2    +      -       -      -
    125N  LEU*     4.8     3.6    +      -       -      +
    127N  SER      3.4    16.9    +      -       -      +
    128N  THR*     3.4    22.4    -      -       -      +
    129N  LEU*     3.8    16.2    -      -       +      -
    130N  ASP*     4.5     1.3    -      -       -      -
    249N  HIS*     4.7    10.8    -      -       -      -
    254N  TYR*     4.3    20.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with SER 122 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92C  GLU*     4.2     6.9    +      -       -      -
    102D  GLU*     3.7    15.4    +      -       -      +
     53N  SER      4.6     1.2    +      -       -      -
     54N  TYR*     3.6    28.3    -      -       -      +
     55N  THR*     4.4     3.7    +      -       -      +
    121N  LYS*     1.3   103.6    +      -       -      +
    123N  SER*     1.3    68.9    +      -       -      +
    124N  ARG*     3.2    21.0    +      -       -      +
    127N  SER*     3.6    23.4    -      -       -      -
    128N  THR      4.4     0.8    +      -       -      -
    130N  ASP*     5.4     2.7    +      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il